BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 026658
(235 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 14/84 (16%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV RH + FV+F +
Sbjct: 205 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFDNE 254
Query: 188 AHAATAMDALQG----QSNIICLS 207
A A DALQG Q+N + +S
Sbjct: 255 VQAGAARDALQGFKITQNNAMKIS 278
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 44/84 (52%), Gaps = 14/84 (16%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV RH + FV+F +
Sbjct: 11 PPN--HILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP--GRHD------IAFVEFDNE 60
Query: 188 AHAATAMDALQG----QSNIICLS 207
A A DALQG Q+N + +S
Sbjct: 61 VQAGAARDALQGFKITQNNAMKIS 84
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 10/72 (13%)
Query: 128 PPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
PP+ LF+ LP + + ++ +F F G+KEVRLV +RH + FV+F +
Sbjct: 6 PPN--QILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP--NRHD------IAFVEFTTE 55
Query: 188 AHAATAMDALQG 199
+ A +ALQG
Sbjct: 56 LQSNAAKEALQG 67
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 135 LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHAATA- 193
LF+ GLP C++ E+ I + K++RLV+ + P G L +V++ + + A+ A
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG----LAYVEYENESQASQAV 75
Query: 194 --MDALQGQSNII 204
MD + + NII
Sbjct: 76 MKMDGMTIKENII 88
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/114 (26%), Positives = 48/114 (42%), Gaps = 16/114 (14%)
Query: 117 GLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKES---RHPG 173
G G +VP +S + V +P ++RE+ +F F K VRL K + H G
Sbjct: 1 GSSGSSGQVP-KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG 59
Query: 174 GDPLILCFVDFVSPAHAATAMDALQGQSNIICLSNLVVFYQIACEYISDKICVH 227
FVDF++ A A +AL C S + ++ E+ ++ V
Sbjct: 60 -----FGFVDFITKQDAKKAFNAL-------CHSTHLYGRRLVLEWADSEVTVQ 101
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ LFV P D E+ IF PF KEV++++ FV+F A
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESA 78
Query: 191 ATAMDALQGQS 201
A A++ + G+S
Sbjct: 79 AKAIEEVHGKS 89
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 36.2 bits (82), Expect = 0.015, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 131 ASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSPAHA 190
+++ LFV P D E+ IF PF KEV++++ FV+F A
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----------FAFVEFEEAESA 51
Query: 191 ATAMDALQGQS 201
A A++ + G+S
Sbjct: 52 AKAIEEVHGKS 62
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 10/94 (10%)
Query: 121 GRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL-VSKESRHPGGDPLIL 179
GR+ + LPP+ + L++ LP + E+ IF + +++R+ + E+R
Sbjct: 1 GRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA------ 54
Query: 180 CFVDFVSPAHAATAMDALQGQSNIICLSNLVVFY 213
+V + A A D L G + +C LVV Y
Sbjct: 55 -YVVYEDIFDAKNACDHLSGFN--VCNRYLVVLY 85
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 12/97 (12%)
Query: 119 GGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLI 178
R+ + LPP+ + L++ LP + E+ IF + +++R+ G P
Sbjct: 5 AAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV--------GNTPET 56
Query: 179 --LCFVDFVSPAHAATAMDALQGQSNIICLSNLVVFY 213
+V + A A D L G + +C LVV Y
Sbjct: 57 RGTAYVVYEDIFDAKNACDHLSGFN--VCNRYLVVLY 91
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 10/96 (10%)
Query: 119 GGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL-VSKESRHPGGDPL 177
R+ + LPP+ + L + LP + E+ IF + +++R+ + E+R
Sbjct: 5 AAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA---- 60
Query: 178 ILCFVDFVSPAHAATAMDALQGQSNIICLSNLVVFY 213
+V + A A D L G + +C LVV Y
Sbjct: 61 ---YVVYEDIFDAKNACDHLSGFN--VCNRYLVVLY 91
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 31.2 bits (69), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 129 PDASST-LFVEGLPSDCSRREVAHIFRPFVGYKEVRLVSKESRHPGGDPLILCFVDFVSP 187
P AS+T L V LP D + RE+ +FR R+ + G FVDF S
Sbjct: 10 PRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRD---YKTGYSFGYAFVDFTSE 66
Query: 188 AHAATAMDALQG 199
+ A+ L G
Sbjct: 67 XDSQRAIKVLNG 78
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 27.3 bits (59), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/90 (22%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 113 DRALGLGGGRSEVPLPPDASSTLFVEGLPSDCSRREVAHIFRPFVGYKEVRL-VSKESRH 171
+++G G + E P + LF+ LP + +++ +F PF ++ + K++
Sbjct: 10 QQSIGAAGSQKEGP----EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN- 64
Query: 172 PGGDPLILC--FVDFVSPAHAATAMDALQG 199
L C FV + +P A A+ ++ G
Sbjct: 65 -----LSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.9 bits (58), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 135 LFVEGLPSDCSRREVAHIFRPFVGYKEVRL-VSKESRHPGGDPLILCFVDFVSPAHAATA 193
LFV L S ++ +F + E+ + ++ P G FV F+ P HA A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG----FAFVTFMFPEHAVKA 66
Query: 194 MDALQGQ 200
+ GQ
Sbjct: 67 YAEVDGQ 73
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.137 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,626,014
Number of Sequences: 62578
Number of extensions: 328023
Number of successful extensions: 593
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 580
Number of HSP's gapped (non-prelim): 19
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)